Syllabus, Biochemistry: Metabolomics and Regulation, 2007
Professor Laura L. Mays Hoopes, office Richard C. Seaver AKA Seaver West 021 (in basement); phone x 66438, email lhoopes@pomona.edu; home phone (909) 621-4738.
Class meetings are 9:00-9:50 MWF starting W, January 17 in SW111 seminar room.
Laboratory meetings are 1:15-5:30 PM on Wednesdays, usually in “the Bond lab” 007 SW, in the basement. The first lab meeting will be Jan 17, but it will be held in SW111 and the ITS building classroom.
Text book is the 6th edition of the Berg, Tymoczko, and Stryer’s Biochemistry
(referred to as BTS below) plus literature papers assigned for metabolomics
discussions.
Sections of the laboratory book on hole-punched paper will be handed out before the
related laboratory sessions. Get a 1” loose leaf notebook to keep lab notes in and
bring it to lab starting Jan 17, so you can take relevant background notes on the
laboratory. You must bring the notebook to every laboratory. Part of the lab grade will be based on properly introducing each experiment with notes from the class discussion plus notes from your readings in the related literature. You need to make predictions about the results; the quality and quantity of predictions will also affect the lab grade. In addition your careful dated notes of procedure changes and data, and your discussion and interpretation of quality control and final data are important in your lab notebook grade.
Grading in Biochemistry is on performance, not on a curve. It is based on:
Three midterms (each counting 15% of the grade) and a final examination (counting 20%
of the grade) on the class work. A sample examination will be posted on the class site for your information about format and style to expect. Borderline class examination grades will be influenced by class participation.
Individual project to create and present to the class a public web page on yeast as a
possible model for human diseases (15%)
Laboratory notebook which will be graded twice during the semester (10% of grade each
time).
Daily class schedule:
Jan 17 W Introduction to Biochemistry with a metabolomics/regulation approach; the
“alphabet of biochemistry”, pKa, pH, and buffers. BTS chap 1.
Jan 19 F No class meeting, day to begin work on web page.
Jan 22 M Review of energetics; free energy, steady state. Review of enzyme kinetics.
BTS chap 2, 8.
Jan 24 W Overview of pathway regulation mechanisms and strategies. Implications of
pathway structure for effective methods of regulation. BTS chap 8, 10.
Jan 26 F Central metabolism; types of metabolic pathways and typical reactions of
specific types of pathways. BTS chap 15.
Jan 29 M Glycolysis and Fermentation part 1 BTS chap 16
Jan 31 W Glycolysis and Fermentation part 2 BTS chap 16
Feb 2 F No class meeting, day to continue work on web page.
Feb 5 M Metabolomic data from glycolysis/fermentation; regulatory analysis case study on cancer cell metabolism. Paper handed out.
Feb 7 W Citric Acid Cycle with anaplerosis and glycoxylate cycle BTS chap 17.
Feb 9 F No class meeting, day to continue work on web page.
Feb 12 M Electron transport and oxidative phosphorylation BTS chap 18
Feb 14 W Krebs Cycle Poker (invented at Caltech). Gamble your grade bonus away.
Feb 16 F No class; use time to work on web page
Feb 19M Pentose phosphate shunt BTS chap 20 (skip the Calvin cycle until later)
Feb 21W Midterm examination 1.
Feb 23F Gluconeogenesis and glycogen biosynthesis BTS chap 16, 21.
Feb 26M Metabolomic data from the citric acid cycle and related pathways Schistosoma mouse model metabolism (paper discussion). Review session.
Feb 28 W Photosynthesis BTS chap 19,20.
Mar 2 F Beta oxidation of fatty acids with electron transport and oxidative
phosphorylation BTS chap 22.1-22.3.
Mar 5 M Fatty acid anabolism connections to central metabolism BTS chap 22.4-22.6
Mar 7 W Synthesis of cholesterol and steroid hormones, connections to central
metabolism BTS chap 26; Regulatory overview of central metabolism of carbohydrates BTS chap 27.
Mar 9 F Midterm examination 2
Mar 12 -16 spring break
Mar 19 M Overview of nitrogenous compound-related biochemical pathways BTS 23.3,
24.1
Mar 21 W Amino acid biosynthesis and catabolism 1 BTS chap 24
Mar 23 F Amino acid biosynthesis and catabolism 2 BTS chap 24
Mar 26 M Nucleotide biosynthesis and catabolism 1 BTS chap 25
Mar 28 W Nucleotide biosynthesis and catabolism 2 BTS chap 25
Mar 30 F Metabolomics and regulation of amino acid and nucleotide pathways; genetic
diseases affecting amino acid and nucleotide metabolism and their regulatory implications, case studies BTS 23.6, 24.4, 25.5
Apr 2 M Catchup/Review session
Apr 4 W Midterm Examination 3
Apr 6 F Principles of assembly of macromolecules: head growth vs tail growth,
activation mechanisms, regulatory implications Handout, no relevant BTS section.
Apr 9 M Glycogen and starch reviewed as examples of macromolecular anabolism;
assembly and catabolism of triglycerides and complex lipids BTS chap 21, 26
Apr 11 W Anabolism of polynucleotides part 1 DNA BTS chap 28
Apr 13 F Anabolism of polynucleotides part 2 RNA BTS chap29 (Take home final
examination for any seniors handed out today, due on or before 5 PM next
Friday).
Apr 16 M Catabolism of polynucleotides Handout, no relevant material in BTS
Apr 18 W Anabolism of proteins part 1. BTS chap 30. John Aris talk at 4-5 PM;
please plan lab work so you can attend
Apr 20 F Anabolism of proteins part 2 BTS chap 30 (Take home examination for any
seniors due today).
Apr 23 M Catabolism of proteins Handout; no relevant material in BTS.
Apr 25 W Macromolecular anabolic and catabolic regulation Part 1: Global regulation of
nucleotide and protein macromolecular synthesis, regulation of turnover, genetic diseases and antibiotics affecting anabolism or catabolism of macromolecules, case studies BTS 28.5, 29.3, 30.7.
Apr 27 F Presentation on genetic disorders of metabolism, day 1
Apr 30 M Presentation on genetic disorders of metabolism, day 2
May 2 W Presentation on genetic disorders of metabolism, day 3
Reading period, TBA: Review session
Final examination as scheduled by Pomona for 9 MWF classes